Merge branch '2.0' into fix-source-text-tumor-descriptor-display

kids-first · Nov 16, 2023 · 4f6c5f9 · 4f6c5f9
2 parents b8b980f + 93f1ab1
commit 4f6c5f9
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Showing 4 changed files with 38 additions and 44 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -53,7 +53,7 @@
     "@apollo/client": "^3.5.10",
     "@dnd-kit/core": "^4.0.3",
     "@dnd-kit/sortable": "^5.1.0",
-    "@ferlab/ui": "^7.14.7",
+    "@ferlab/ui": "^7.14.8",
     "@loadable/component": "^5.15.2",
     "@react-keycloak/core": "^3.2.0",
     "@react-keycloak/web": "^3.4.0",

diff --git a/src/locales/en.ts b/src/locales/en.ts
@@ -1511,25 +1511,31 @@ const en = {
       family_id: 'Family ID',
       family_relationship: 'Family Relationship',
       family_unit: 'Family Composition',
+      hpo_phenotype_observed: 'Observed Phenotype (HPO)',
       hpo_term: 'HPO Term',
       hpo_term_tooltip: '# of participants with this exact HPO term',
       interpretation: 'Interpretation',
       mondo_diagnosis: 'Diagnosis (MONDO)',
       mondo_term: 'MONDO Term',
       mondo_term_tooltip: '# of participants with this exact MONDO term',
+      nb_biospecimens: 'Biospecimens',
+      nb_files: 'Files',
       not_observed: 'Not observed',
       observed: 'Observed',
       other: 'Other',
       participant_id: 'Participant ID',
       pedcBioPortal: 'PedcBioPortal',
       phenotype: 'Phenotype',
       phenotype_hpo: 'Phenotype (HPO)',
+      phenotypes_hpo_not_observed: 'Not Observed Phenotype (HPO)',
       phenotype_source_text: 'Phenotype (Source Text)',
       proband: 'Proband',
       proband_only: 'Proband-only',
       profile: 'Profile',
       race: 'Race',
       sex: 'Sex',
+      source_text_phenotype: 'Observed Phenotype (Source Text)',
+      study: 'Study',
       trio: 'Trio',
       trio_plus: ' Trio+',
       trisomy: 'T21: "Trisomy 21"',

diff --git a/src/views/DataExploration/components/PageContent/tabs/Participants/index.tsx b/src/views/DataExploration/components/PageContent/tabs/Participants/index.tsx
@@ -1,4 +1,5 @@
 import React, { useEffect, useState } from 'react';
+import intl from 'react-intl-universal';
 import { useDispatch } from 'react-redux';
 import { Link } from 'react-router-dom';
 import { DownloadOutlined } from '@ant-design/icons';
@@ -49,7 +50,6 @@ import {
 import { mapStudyToPedcBioportal } from 'views/Studies/utils/helper';
 
 import { TABLE_EMPTY_PLACE_HOLDER } from 'common/constants';
-import OutcomesAgeCells from 'components/OutcomesAgeCells';
 import { ReportType } from 'services/api/reports/models';
 import { SetType } from 'services/api/savedSet/models';
 import { fetchReport, fetchTsvReport } from 'store/report/thunks';
@@ -65,10 +65,10 @@ interface OwnProps {
   sqon?: ISqonGroupFilter;
 }
 
-const defaultColumns: ProColumnType[] = [
+const getDefaultColumns = (): ProColumnType[] => [
   {
     key: 'participant_id',
-    title: 'Participant ID',
+    title: intl.get('entities.participant.participant_id'),
     dataIndex: 'participant_id',
     sorter: {
       multiple: 1,
@@ -79,7 +79,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'study.study_code',
-    title: 'Study',
+    title: intl.get('entities.participant.study'),
     sorter: {
       multiple: 1,
     },
@@ -89,7 +89,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'study_external_id',
-    title: 'dbGaP',
+    title: intl.get('entities.participant.dbgap'),
     dataIndex: 'study_external_id',
     render: (study_external_id: string) =>
       study_external_id ? (
@@ -104,7 +104,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'is_proband',
-    title: 'Proband',
+    title: intl.get('entities.participant.proband'),
     dataIndex: 'is_proband',
     sorter: {
       multiple: 1,
@@ -114,7 +114,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'sex',
-    title: 'Sex',
+    title: intl.get('entities.participant.sex'),
     dataIndex: 'sex',
     sorter: {
       multiple: 1,
@@ -128,7 +128,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'diagnosis.mondo_id_diagnosis',
-    title: 'Diagnosis (MONDO)',
+    title: intl.get('entities.participant.mondo_diagnosis'),
     dataIndex: 'diagnosis',
     className: styles.diagnosisCell,
     render: (diagnosis: IArrangerResultsTree<IParticipantDiagnosis>) => {
@@ -162,7 +162,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'phenotype.hpo_phenotype_observed',
-    title: 'Observed Phenotype (HPO)',
+    title: intl.get('entities.participant.hpo_phenotype_observed'),
     dataIndex: 'phenotype',
     className: styles.phenotypeCell,
     render: (phenotype: IArrangerResultsTree<IParticipantPhenotype>) => {
@@ -196,7 +196,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'families_id',
-    title: 'Family ID',
+    title: intl.get('entities.participant.family_id'),
     dataIndex: 'families_id',
     sorter: {
       multiple: 1,
@@ -205,7 +205,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'family_type',
-    title: 'Family Composition',
+    title: intl.get('entities.participant.family_unit'),
     dataIndex: 'family_type',
     sorter: {
       multiple: 1,
@@ -215,7 +215,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'pedcbioportal',
-    title: 'PedcBioPortal',
+    title: intl.get('entities.participant.pedcBioPortal'),
     sorter: {
       multiple: 1,
     },
@@ -237,7 +237,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'nb_biospecimens',
-    title: 'Biospecimens',
+    title: intl.get('entities.participant.nb_biospecimens'),
     sorter: {
       multiple: 1,
     },
@@ -272,7 +272,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'nb_files',
-    title: 'Files',
+    title: intl.get('entities.participant.nb_files'),
     sorter: {
       multiple: 1,
     },
@@ -304,7 +304,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'race',
-    title: 'Race',
+    title: intl.get('entities.participant.race'),
     dataIndex: 'race',
     defaultHidden: true,
     sorter: {
@@ -314,7 +314,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'ethnicity',
-    title: 'Ethnicity',
+    title: intl.get('entities.participant.ethnicity'),
     dataIndex: 'ethnicity',
     defaultHidden: true,
     sorter: {
@@ -324,7 +324,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'external_id',
-    title: 'Participant External ID',
+    title: intl.get('entities.participant.external_id_tooltip'),
     dataIndex: 'external_id',
     defaultHidden: true,
     sorter: {
@@ -334,7 +334,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'diagnosis.ncit_id_diagnosis',
-    title: 'Diagnosis (NCIT)',
+    title: intl.get('entities.participant.diagnosis_NCIT'),
     dataIndex: 'diagnosis',
     defaultHidden: true,
     sorter: {
@@ -363,7 +363,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'diagnosis.source_text',
-    title: 'Diagnosis (Source Text)',
+    title: intl.get('entities.participant.diagnosis_source_text'),
     dataIndex: 'diagnosis',
     defaultHidden: true,
     render: (mondo: IArrangerResultsTree<IParticipantDiagnosis>) => {
@@ -383,7 +383,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'outcomes.vital_status',
-    title: 'Vital Status',
+    title: intl.get('entities.participant.vital_status'),
     dataIndex: 'outcomes',
     defaultHidden: true,
     sorter: {
@@ -397,7 +397,7 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'phenotypes_hpo_not_observed',
-    title: 'Not Observed Phenotype (HPO)',
+    title: intl.get('entities.participant.phenotypes_hpo_not_observed'),
     dataIndex: 'phenotype',
     defaultHidden: true,
     sorter: {
@@ -407,26 +407,14 @@ const defaultColumns: ProColumnType[] = [
   },
   {
     key: 'source_text_phenotype',
-    title: 'Observed Phenotype (Source Text)',
+    title: intl.get('entities.participant.source_text_phenotype'),
     dataIndex: 'phenotype',
     defaultHidden: true,
     sorter: {
       multiple: 1,
     },
     render: () => TABLE_EMPTY_PLACE_HOLDER,
   },
-  {
-    key: 'outcomes.age_at_event_days.value',
-    title: 'Age at Outcome',
-    dataIndex: 'outcomes',
-    defaultHidden: true,
-    sorter: {
-      multiple: 1,
-    },
-    render: (outcomes: IArrangerResultsTree<IParticipantOutcomes>) => (
-      <OutcomesAgeCells outcomes={outcomes} />
-    ),
-  },
 ];
 
 const ParticipantsTab = ({ sqon }: OwnProps) => {
@@ -530,7 +518,7 @@ const ParticipantsTab = ({ sqon }: OwnProps) => {
   return (
     <ProTable<ITableParticipantEntity>
       tableId="participants_table"
-      columns={defaultColumns}
+      columns={getDefaultColumns()}
       wrapperClassName={styles.participantTabWrapper}
       loading={results.loading}
       initialColumnState={userInfo?.config.data_exploration?.tables?.participants?.columns}
@@ -569,7 +557,7 @@ const ParticipantsTab = ({ sqon }: OwnProps) => {
           dispatch(
             fetchTsvReport({
               columnStates: userInfo?.config.data_exploration?.tables?.participants?.columns,
-              columns: defaultColumns,
+              columns: getDefaultColumns(),
               index: INDEXES.PARTICIPANT,
               sqon: getCurrentSqon(),
             }),